Tubercidin (CED0009729)

Record Information

Version

1.0

Creation Date

2026-03-31 20:49:13 UTC

Update Date

2026-05-14 17:48:25 UTC

SynCED ID

CED0009729

Secondary Accession Numbers

CHEM057872

Identification

Common Name

Tubercidin

Class

Small Molecule

Description

Tubercidin is an organic compound with the chemical formula C11H14N4O4 and an average molecular weight of 266.26 g/mol. Tubercidin belongs to the pyrrolopyrimidine nucleosides and nucleotides, a class of nucleosides, nucleotides, and analogues within the organic compounds. This compound is found in or released from five recorded sources, including antibiotics within healthcare, pharmaceuticals, and veterinary products. It is also associated with household cleaning and consumer products, specifically soap detergents and perfumes within detergents and soaps, as well as electrical and electronic equipment, specifically thin magnetic films and conductors or conductive bodies characterised by the conductive materials. Recorded routes of exposure for this substance include oral and inhalation pathways. Regarding its biological activity, there is one recorded protein target: the DeoD-type purine nucleoside phosphorylase (deoD).

Contaminant Type

Not Available

Chemical Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
7-Deazaadenosine	ChEBI
Sparsomycin a	ChEBI
7 Deazaadenosine	MeSH
4-Amino-7 beta-D-ribofuranosyl-7H-pyrrolo(2,3-D)pyrimidine	MeSH
Deazaadenosine	MeSH

Chemical Formula

C₁₁H₁₄N₄O₄

Average Molecular Mass

266.257 g/mol

Monoisotopic Mass

266.102 g/mol

CAS Registry Number

69-33-0

IUPAC Name

(2R,3R,4S,5R)-2-{4-amino-7H-pyrrolo[2,3-d]pyrimidin-7-yl}-5-(hydroxymethyl)oxolane-3,4-diol

Traditional Name

tubercidin

SMILES

NC1=C2C=CN([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)C2=NC=N1

InChI Identifier

InChI=1S/C11H14N4O4/c12-9-5-1-2-15(10(5)14-4-13-9)11-8(18)7(17)6(3-16)19-11/h1-2,4,6-8,11,16-18H,3H2,(H2,12,13,14)/t6-,7-,8-,11-/m1/s1

InChI Key

HDZZVAMISRMYHH-KCGFPETGSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrrolopyrimidine nucleosides and nucleotides. These are nucleoside derivatives containing a ribose derivative which is n-glycosylated to a pyrrolopyrimidine. Also called deazapurine nucleosides, they are analogs of purine nucleosides with the N atom of the purine being replaced by a C atom at position 7.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrrolopyrimidine nucleosides and nucleotides

Sub Class

Not Available

Direct Parent

Pyrrolopyrimidine nucleosides and nucleotides

Alternative Parents

Substituents

Pyrrolopyrimidine ribonucleoside
Glycosyl compound
N-glycosyl compound
Pentose monosaccharide
Pyrrolo[2,3-d]pyrimidine
Pyrrolopyrimidine
Aminopyrimidine
Monosaccharide
Pyrimidine
Imidolactam
Substituted pyrrole
Heteroaromatic compound
Pyrrole
Tetrahydrofuran
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Primary alcohol
Alcohol
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Organopnictogen compound
Organic oxygen compound
Primary amine
Amine
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

N-glycosylpyrrolopyrimidine (CHEBI:45836 )

Biological Properties

Status

Detected and Not Quantified

Origin

Not Available

Cellular Locations

Not Available

Biofluid Locations

Not Available

Tissue Locations

Not Available

Applications

Not Available

Biological Roles

antimetabolite (PMC9693223 )?A chemical that inhibits the use of a metabolite, which is another chemical that is part of normal metabolism
inhibitor (PMC1904411 )?

Chemical Roles

Not Available

Organoleptic Effects

Not Available

Physical Properties

State

Not Available

Appearance

Not Available

Experimental Properties

Property	Value
Melting Point	Not Available
Boiling Point	Not Available
Solubility	Not Available

Predicted Properties

Property	Value	Source
Water Solubility	16.6 g/L	ALOGPS
logP	-0.83	ALOGPS
logP	-1.3	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	12.46	ChemAxon
pKa (Strongest Basic)	7.2	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	126.65 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	65.37 m³·mol⁻¹	ChemAxon
Polarizability	25.62 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum	splash10-00bm-9550000000-16876c0a7138908cbdda	Not Available	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum	splash10-000i-0900000000-36d410d303827e6de6d9	Not Available	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum	splash10-000i-0900000000-36d410d303827e6de6d9	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-00kr-0960000000-1a5e02593ed83cb531cd	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-000i-1910000000-7cc0105828de928ddcf6	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-000i-2900000000-369f974973fc879a7824	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-0159-0690000000-1ae582cae83a006db24d	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-001i-0910000000-96ad7decf39fc934a27c	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-0kai-2900000000-fcb5b39379ac9b95b344	Not Available	View Spectrum

Toxicity Profile

Toxicity Values

Toxicity Value	Organism	Dose Descriptor	Route of Exposure	Predicted or Experimental	Toxicity Rating	Reference
272.0 Log mg/kg [150:480]	Rat	LD50	oral	predicted	Not Available	Not Available

Toxicity / Toxin Class

Not Available

Mechanism of Toxicity

Not Available

Carcinogenicity (IARC Classification)

Not Available

Minimum Risk Level

Not Available

Symptoms

Not Available

Treatment

Not Available

Health Effects

Health Effect	Relationship	Direction	Description	Reference

Exposure Sources

Source ID	Source	Sector	Reference
CEDs000306	Antibiotics?Antibiotics are synthetic or semi-synthetic compounds used to treat bacterial infections in humans and animals.	Healthcare, pharmaceuticals & veterinary products	Not Available
CEDs000511	Conductors Or Conductive Bodies Characterised By The Conductive Materials?Conductors, or conductive bodies, are materials that allow the flow of electrical current, typically made from metals such as copper, aluminum, or silver.	Electrical & Electronic Equipment	PubChem
CEDs000538	Thin Magnetic Films?Thin magnetic films are layers of magnetic material ranging from a few nanometers to several micrometers in thickness, commonly used in applications such as magnetic sensors, data storage devices, and electronic components.	Electrical & Electronic Equipment	PubChem
CEDs000561	Perfumes Within Detergents And Soaps?Perfumes within detergents and soaps are synthetic fragrance compounds added to enhance the sensory experience of cleaning products.	Household cleaning & consumer products	PubChem
CEDs000563	Soap Detergents?Soap detergents are synthetic surfactants designed to enhance the cleaning efficacy of water by reducing surface tension, allowing for better interaction with dirt and grease.	Household cleaning & consumer products	PubChem
CEDs000600	Herbicides And Algicides?Herbicides and algicides are synthetic chemicals primarily used to control unwanted plants and algae in various environments.	Agriculture & land management	PubChem
CEDs000610	Aftersun Products?Aftersun products are designed to soothe and hydrate the skin after sun exposure, often containing various synthetic chemicals such as emollients, preservatives, and fragrances.	Personal care & cosmetics	PubChem
CEDs000611	Anti Perspirants Or Body Deoderants?Antiperspirants and body deodorants commonly contain synthetic chemicals such as aluminum compounds, parabens, and synthetic fragrances.	Personal care & cosmetics	PubChem
CEDs000615	Eye Makeup Products?Eye makeup products, including mascaras, eyeliners, and eyeshadows, often contain a variety of synthetic chemicals such as pigments, preservatives, and film-forming agents.	Personal care & cosmetics	PubChem
CEDs000642	Footwear?Footwear production often involves the use of various synthetic chemicals, such as adhesives, dyes, and treatments, which can contribute to environmental contamination.	Textiles, leather & furnishings	PubChem
CEDs000685	Ceramics?Ceramics can be a source of synthetic chemical contamination through various additives and processing agents used in their production.	Building & Construction	PubChem
CEDs000696	Nanotechnology?Nanotechnology involves the manipulation of materials at the molecular or atomic level, typically within the range of 1 to 100 nanometers.	Industrial manufacturing & chemical processing	PubChem
CEDs000698	Jewellery?Jewellery production often involves the use of various synthetic chemicals during the extraction and processing of metals.	Mining & metal processing	PubChem
CEDs000739	Inks?Inks are complex mixtures composed of pigments or dyes, solvents, resins, and additives used primarily for printing and writing applications.	Paper, pulp & fiber products	PubChem

Pathways

0 pathwaysPathway Source: PathBank

No pathways found

No metabolic pathways have been associated with this synthetic chemical

Targets

Structure	Protein	UniProt ID	Organism	Relationship	Details
Click to view 3D structure	Adenosine kinase	P55263	Humans	Predicted (SEA)	Prediction Confidence Score 0.693 Applicability Domain 1.0 Statistical Significance 1.00e-05 Supporting Reference Compounds 22 E-value 0.0778492
Click to view 3D structure	Adenosine kinase	P9WID4	Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)	Predicted (SEA)	Prediction Confidence Score 0.655 Applicability Domain 0.68 Statistical Significance 2.00e-05 Supporting Reference Compounds 2 E-value 0.155698
Click to view 3D structure	Adenosine kinase	A5U4N0	Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra)	Predicted (SEA)	Prediction Confidence Score 0.608 Applicability Domain 0.608 Statistical Significance 8.00e-05 Supporting Reference Compounds 1 E-value 0.622794
Click to view 3D structure	NS5	A0A143MHK7	Zika virus	Predicted (SEA)	Prediction Confidence Score 0.548 Applicability Domain 1.0 Statistical Significance 1.00e-05 Supporting Reference Compounds 10 E-value 0.0778492
Click to view 3D structure	Adenosine receptor A1	P25099	Rattus norvegicus	Predicted (SEA)	Prediction Confidence Score 0.544 Applicability Domain 0.646 Statistical Significance 0.0019 Supporting Reference Compounds 221 E-value 15.0249
Click to view 3D structure	Adenosine receptor A2a	P30543	Rattus norvegicus	Predicted (SEA)	Prediction Confidence Score 0.541 Applicability Domain 0.646 Statistical Significance 0.0018 Supporting Reference Compounds 174 E-value 13.8572
Click to view 3D structure	Adenosine receptor A3	P0DMS8	Humans	Predicted (SEA)	Prediction Confidence Score 0.535 Applicability Domain 0.646 Statistical Significance 0.0027 Supporting Reference Compounds 391 E-value 21.0193
Click to view 3D structure	Adenosine receptor A3	P28647	Rattus norvegicus	Predicted (SEA)	Prediction Confidence Score 0.535 Applicability Domain 0.646 Statistical Significance 0.0013 Supporting Reference Compounds 71 E-value 10.1982
Click to view 3D structure	Heat shock protein HSP 90-alpha	P07900	Humans	Predicted (SEA)	Prediction Confidence Score 0.533 Applicability Domain 0.646 Statistical Significance 5.90e-04 Supporting Reference Compounds 109 E-value 4.5931
Click to view 3D structure	Endoplasmin	P14625	Humans	Predicted (SEA)	Prediction Confidence Score 0.533 Applicability Domain 0.646 Statistical Significance 4.20e-04 Supporting Reference Compounds 31 E-value 3.26967
Click to view 3D structure	Adenosine receptor A2a	P29274	Humans	Predicted (SEA)	Prediction Confidence Score 0.512 Applicability Domain 0.646 Statistical Significance 0.0031 Supporting Reference Compounds 303 E-value 24.289
Click to view 3D structure	Adenosine receptor A1	P30542	Humans	Predicted (SEA)	Prediction Confidence Score 0.506 Applicability Domain 0.646 Statistical Significance 0.0031 Supporting Reference Compounds 302 E-value 23.8219
Click to view 3D structure	Adenosine kinase	P9WID5	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Predicted (SEA)	Prediction Confidence Score 0.504 Applicability Domain 0.608 Statistical Significance 5.00e-05 Supporting Reference Compounds 4 E-value 0.389246
Click to view 3D structure	Adenosine receptor A1	P47745	Cavia porcellus	Predicted (SEA)	Prediction Confidence Score 0.484 Applicability Domain 0.646 Statistical Significance 8.40e-04 Supporting Reference Compounds 38 E-value 6.53933
Click to view 3D structure	Histone-lysine N-methyltransferase, H3 lysine-79 specific	Q8TEK3	Humans	Predicted (SEA)	Prediction Confidence Score 0.476 Applicability Domain 0.608 Statistical Significance 5.00e-04 Supporting Reference Compounds 18 E-value 3.89246
Click to view 3D structure	Adenosine receptor A2b	P29275	Humans	Predicted (SEA)	Prediction Confidence Score 0.47 Applicability Domain 0.646 Statistical Significance 0.0033 Supporting Reference Compounds 187 E-value 25.7681
Click to view 3D structure	High affinity choline transporter 1	Q9GZV3	Humans	Predicted (SEA)	Prediction Confidence Score 0.459 Applicability Domain 0.646 Statistical Significance 3.90e-04 Supporting Reference Compounds 75 E-value 3.03612
Click to view 3D structure	Solute carrier family 28 member 3	Q9HAS3	Humans	Predicted (SEA)	Prediction Confidence Score 0.453 Applicability Domain 0.646 Statistical Significance 2.00e-05 Supporting Reference Compounds 3 E-value 0.155698
Click to view 3D structure	Adenosine deaminase	P56658	Bos taurus	Predicted (SEA)	Prediction Confidence Score 0.451 Applicability Domain 0.509 Statistical Significance 3.70e-04 Supporting Reference Compounds 17 E-value 2.88042
Click to view 3D structure	S-methyl-5'-thioadenosine phosphorylase	Q9CQ65	Mus musculus	Predicted (SEA)	Prediction Confidence Score 0.45 Applicability Domain 0.45 Statistical Significance 5.70e-04 Supporting Reference Compounds 1 E-value 4.43741
Click to view 3D structure	Adenosine receptor A1	P49892	Gallus gallus	Predicted (SEA)	Prediction Confidence Score 0.449 Applicability Domain 0.475 Statistical Significance 7.60e-04 Supporting Reference Compounds 6 E-value 5.91654
Click to view 3D structure	Adenosine receptor A1	P28190	Bos taurus	Predicted (SEA)	Prediction Confidence Score 0.446 Applicability Domain 0.491 Statistical Significance 0.002 Supporting Reference Compounds 72 E-value 15.6477
Click to view 3D structure	NAD kinase	Q5HH78	Staphylococcus aureus (strain COL)	Predicted (SEA)	Prediction Confidence Score 0.443 Applicability Domain 0.443 Statistical Significance 3.80e-04 Supporting Reference Compounds 1 E-value 2.95827
Click to view 3D structure	NAD kinase 1	Q8Y8D7	Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)	Predicted (SEA)	Prediction Confidence Score 0.443 Applicability Domain 0.443 Statistical Significance 3.80e-04 Supporting Reference Compounds 1 E-value 2.95827
Click to view 3D structure	Adenosine kinase	Q9TVW2	Toxoplasma gondii	Predicted (SEA)	Prediction Confidence Score 0.442 Applicability Domain 0.646 Statistical Significance 3.60e-04 Supporting Reference Compounds 5 E-value 2.80257